MAP1A p.Gly482=
c.1446A>G · rs55941117 · VCV717737
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.25%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP -3.1 |
| Overall | ||
| CADD | 5.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.25%
European (non-Finnish) · 2,955/1,179,794 alleles
Filtering AF
0.243%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.24%
Overall
0.2%
3,228/1,613,686 alleles · rare
exomes 3,004/1,461,458 · genomes 224/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.25% | 399 |
| Remaining individualsnot grpmax-eligible | 0.141% | 710 |
| Finnishnot grpmax-eligible | 0.109% | 915 |
| Admixed American | 0.0868% | 1,152 |
| African / African-American | 0.0613% | 1,631 |
| South Asian | 0.0165% | 6,068 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,792 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- MAP1A
- Protein
- p.Gly482=
- Coding
- c.1446A>G
- MANE Select
- NM_002373
- dbSNP
- rs55941117
- Type
- single nucleotide variant
- Location
- chr15:43522919 (GRCh38)
- Structure
- AlphaFold pLDDT 94.44 · 41 PDB
Similar variants
- MAP1A p.Arg2734Gln Uncertain significance ★★ same type
- MAP1A p.Gly567Ala Uncertain significance ★★ ⚠ same type
- MAP1A p.Leu1621Val Benign ★★ same type
- MAP1A p.Ser1152= Likely benign ★★ same type
- MAP1A p.Ser1311= Benign/Likely benign ★★ same type
- MAP1A p.Ser1544= Benign ★★ same type
- MAP1A p.Ser1858Cys Likely benign ★★ same type
- MAP1A p.Ser2152= Likely benign ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/map1a-p-gly482 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown